Attempts have been made to not only clarify gene structures of a wide variety of organisms but also elucidate gene functions at a genomic level. Also, technique for efficiently analyzing gene function has been rapidly developed. A microarray refers to an array prepared by highly densely aligning and immobilizing a number of polynucleotides in every predetermined region on a carrier such as a slide glass and is very usefully used for determining the nucleotide sequence of a gene and simultaneously analyzing e.g., gene expression, mutation and polymorphism. Analysis for genetic information using the microarray is extremely useful for e.g., studies for drug development, disease diagnosis and development of preventive methods.
In the detection using a microarray, first, a target polynucleotide labeled with a radioactive isotope or a fluorescence dye is hybridized with probe polynucleotides highly densely aligned on the surface of a carrier. The target polynucleotide, which has a complementary nucleotide sequence to the probe polynucleotide, complementarily hybridizes with the probe polynucleotide; however, a polynucleotide failed to hybridize is removed by washing.
In the detection of hybridization using a microarray, a decision error may occur due to performance degradation, insufficient washing or the like in each microarray. However, whether the decision is error or not is determined at the discretion of the user who operates the microarray and thus quite ambiguous. In the circumstances, it has been impossible to process a large number of samples in an automatic apparatus constituted of a detector and a reactor in combination.
In the method described in Patent Document 1, to eliminate a decision error that occurs when the brightness of a spot is equal to or lower than a lower detection limit of a detector, or equal to or higher than an upper detection limit thereof, a microarray spotted with probe DNAs different in concentration is used and determination is made only based on the results from spots having brightness within a predetermined range. However, in this method, performance degradation, insufficient washing and the like in each microarray cannot be detected.
In the method described in Patent Document 2, a marker substance is covalently bonded to a probe array and the position of a spot of each probe is rapidly and accurately specified based on the position of the marker substance. However, in the method, performance degradation, insufficient washing and the like in each probe array can be detected; however, the occurrence of hybridization failure and PCR failure cannot be detected.